So I've been trying to build and load a package and have been getting this error
devtools::document(roclets=c('rd', 'collate', 'namespace'))
Updating stat290.ass2 documentation
Loading stat290.ass2
Error in file(con, "r") : cannot open the connection
Calls: suppressPackageStartupMessages ... topic_add_examples -> read_lines -> <Anonymous> -> file
In addition: Warning message:
In file(con, "r") :
cannot open file 'C:\Users\blah\Desktop\stat290.ass2': Permission denied
Execution halted
Exited with status 1.
I've seen these posts as reference: Roxygen Warning "cannot open the connection" "Permission Denied", https://github.com/klutometis/roxygen/issues/766, but they say the error has been patched out. I have tried deleting and re-installing both devtools and roxygen2, but have not had any luck
I resolved this issue by removing the #return and #example in my roxygen2 comments at the header of the function as I did not write anything in for them. It appears that if you put a #XXX you need to fill in the information next to it, otherwise the key is missing the value and it bombs.
I got he idea from the error topic_add_examples -> read_lines -> since it appeared it was trying to read the comments next to my #example but I didn't have any.
Related
I was running the check for my package that I have created when I got this error due to some example file that has been created outside my package directory which has been created due to the vignette I have created because while checking when R was reading the vignette, it got this error and I tried to delete the folder that has been created outside my package directory but I am not able to. Here is the error that is shown while checking the package:
E checking examples ... Running examples in 'ikpack-Ex.R' failed
Warning in file(con, "r") :
cannot open file 'ikpack-Ex.Rout': Permission denied Error in file(con, "r") : cannot open the connection Execution halted
Any kind of help related to this is appreciated.
I upgraded to R 4.0.2 today, and also updated my copy of RStudio. While I've been updating my packages I've found that shiny won't install. Whenever I try to install shiny I get the following message...
Error in as.list.environment(base::getNamespace("shiny"), all.names = TRUE) :
lazy-load database 'H:/My Documents/R/win-library/4.0/shiny/R/shiny.rdb' is corrupt
Calls: <Anonymous> ... withCallingHandlers -> <Anonymous> -> <Anonymous> -> as.list.environment
Execution halted
*** arch - x64
Error in as.list.environment(base::getNamespace("shiny"), all.names = TRUE) :
lazy-load database 'H:/My Documents/R/win-library/4.0/shiny/R/shiny.rdb' is corrupt
Calls: <Anonymous> ... withCallingHandlers -> <Anonymous> -> <Anonymous> -> as.list.environment
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'H:/My Documents/R/win-library/4.0/shiny'
Warning in install.packages :
installation of package ‘shiny’ had non-zero exit status
I get this error regardless of whether I just type "install.packages('shiny')" and peace out or if I download the tar.gz and try to install from a local directory. The same error happens when I specify to download an older version of shiny, so I'm pretty sure it's not a problem with the file I'm trying to install. Restarting RStudio does nothing, which is the only advice I could find online for shiny installation problems.
Has anyone else had any problems with installing shiny since upgrading to the newest version of R? Any workarounds?
I am unable to install any package due to the error mentioned in the title.
I attempt to run the following package :
install.packages("tseries")
However, I then receive the error:
Warning in install.packages 'lib = "C:/Users/santi/OneDrive/Documents/R"' is not writable :
Afterwards, I receive the following pop message:
I proceed to click "yes" bu then I get the following error:
Warning in install.packages cannot create dir 'C:\Users\santi\OneDrive\Documents\R\win-library\3.5\file64444b1a3a3b', reason 'No such file or directory'
I want to be clear that I am using my personal computer and all my settings are set to administrator and I have set all my premissions to my account to "Allow"
I am having a problem I think I may be able to solve my if I could deinstall 'ggplotly' before attempting to reinstall it.
Here's what happened:
Code that worked fine when an instructor demoed it, failed when I tried it at home. It was R Markdown. Investigating the problem code cell line by line, the problem was centered around ggplot2 (which uses ggplotly). Code and error messages are provided below. In the code "graph" was a ggplot2 facet_wrap() that was supposed to pass into ggplotly.
Here is the excerpt from my console of the problem and a failed attempt to fix it by re-installing:
> ggplotly(graph)
Error in dev_fun(tmpPlotFile, width = deviceWidth, height = deviceHeight) :
unable to start png() device
> ggplotly(graph)
Error in RStudioGD() :
Shadow graphics device error: r error 4 (R code execution error)
In addition: Warning messages:
1: In grDevices:::png("C:/Users/User/AppData/Local/Temp/Rtmp0ar20f/3b613ba7d0ce4228bc937aee7cfcb112.png", :
unable to open file 'C:/Users/User/AppData/Local/Temp/Rtmp0ar20f/3b613ba7d0ce4228bc937aee7cfcb112.png' for writing
2: In grDevices:::png("C:/Users/User/AppData/Local/Temp/Rtmp0ar20f/3b613ba7d0ce4228bc937aee7cfcb112.png", :
opening device failed
> install.packages("plotly")
Error in install.packages : Updating loaded packages
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
cannot open compressed file 'C:\Users\User\AppData\Local\Temp\Rtmp0ar20f/libloc_190_4464fd2b.rds', probable reason 'No such file or directory
As per comments on this thread, a package can be de-installed with remove.packages. As per the original problem on this post, de-installing and re-installing cleared it, but for completeness, here are all the precautions I took to improve the chances of this working:
removed the package as indicated
re-initialized RStudio (exited without saving the workspace and re-entered it)
By default, it remembered some of my environment so I clicked the broom icon to clear out all variables and data from memory
re-installed the package
re-loaded the original R file and tested to make sure all worked as expected.
This is what I saw in the console with de-installing and re-installing in contrast to the messages shown on the original post:
During de-installation:
> remove.packages("plotly")
Removing package from ‘C:/ProgramFilesCoders/R/R-3.3.2/library’
(as ‘lib’ is unspecified)
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
cannot open compressed file 'C:\Users\User\AppData\Local\Temp\Rtmp0ar20f/libloc_190_4464fd2b.rds', probable reason 'No such file or directory'
During re-installation:
> install.packages("plotly")
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/plotly_4.5.6.zip'
Content type 'application/zip' length 817502 bytes (798 KB)
downloaded 798 KB
package ‘plotly’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\User\AppData\Local\Temp\RtmpGco6OK\downloaded_packages
In an R package, I have a figure (jpeg) located under man/figures, which is added to a Rd file with,
\if{html}{\figure{supplydemand.jpg}{Supply-demand}}
\if{latex}{\figure{supplydemand}{Supply-demand}}
After updating to roxygen2 4.0.1, I get the error:
==> roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))
Error in file(con, "r") : cannot open the connection
Calls: suppressPackageStartupMessages ... <Anonymous> -> first_time -> vapply -> FUN -> readLines -> file
In addition: Warning message:
In file(con, "r") : cannot open file './man/figures': Permission denied
Execution halted
Exited with status 1.
If I remove the code to insert the figure, I still get this error. Only when I remove the subdir man/figures does roxygen2 work OK.
I assume this is a bug in roxygen2 or is there a workaround?